Whole brain image analysis

I’m developing tools for the analysis and visualisation of whole brain microscopy images. This includes:

  • cellfinder for 3D cell detection
  • amap for 3D registration and atlas-based segmentation
  • neuro for volumetric analysis of brain structures and visualisation

Further information is on the website.

For 3D visualisation, I’ve also contributed to Federico Claudi’s excellent brainrender (you can check out the paper at bioRxiv).